NOTE: the best way to figure out what you need to work on is to do 'Ctrl+F' and search for your name. Hit 'enter' to find the next instance. - Thanks, Dr. B
----- this assumes I haven't misspelled your name!
'Starter Questions' for the TEAM meetings - to help your students get to know you better
QUESTIONS FOR THE WHOLE GROUP
Favorite place on the Drag (or around the 40 acres but not on campus)?
Where are you from? What high school did you go to?
How is your adjustment to UT going?
Favorite/Least favorite [[#|classes this]] semester? Any particular classes you are concerned about?
What are your majors?
What are your career interests?
What do you think of VDS so far? Favorite aspects? Least favorite aspects?
Which do you prefer - wet lab or computer labs?
Do you have any concerns about the labs?
Do you have any questions regarding the concepts underlying the labs?
What do you hope to get out of this experience?
What are your research interests?
Since this is VDS, what is your favorite drug/molecule?
General points to cover (by the TEAM leaders):
- basic intro (major, year, etc.)
- overview of what they can expect from VDS (short- and long-term)
- how VDS has helped you and why it is beneficial for them to stick with it
- your research interests and experiences
- your career plans and what stage you are at now
- Why VDS is the best stream!
Printer Installation
Login as Mentor, Start Menu,
Devices And printers
Add New Printer
Add "local" printer
Create New Port --> standard TCP pathway
Enter IP 128.82.195.186
Printer Name Lexmark C543
Add Printer (if can't find printer do Window Update)
For installation of a different Printer (such as Dell) change the IP address and Printer Name
Saturday 2.16
-NaOH and Tris
(from the first lab)
1L each
SATURDAY (2/2)
Make the different Stock and Dilutions for Beer's Law Unknown Experiment - Urvashi
Thao and Urvashi - I placed extra Ink, toner and paper for the Printer in the lab so that the students can print their PyMol assignment - Thanks, Dr. B
@5pm - close lab and check if any are missing labnotebooks (if they are - put a note on the LabNotebookGrading_VDS_Sp13 spreadsheet on GDocs for VDSstaff@gmail.com (use mentor password)
.
ANYTIME
Test VS3 protocol - Christina (a non CS person will do it next)
Make Mini-Research Write Up Wikipages for each student (use their Disease name as the name of the page)
Create Voting forms for MiniResearch Wiki Assign
Update the Google Site for VDS - Larry
- put new Forum posters there.
Check your growth of pGBR22 in BL21(DE3) from overnight as a test for 'purple' color - (check today and tomorrow - how long does it take to go purple?) -
Grow up pGBR22 in BL21(DE3) overnight in Kan as a test for 'purple' color (start this late at the end of your shift)
Wikispaces
Make a 'bracket' by Teams for doing MiniResearch WriteUp Wiki assign competition -Christina
Mini Research Wiki post templates - can do this after we have chosen all of the Diseases - Christina
'20 questions' form - can do this after we have chosen all of the Diseases
Embed Google Spreadsheet into Wikispaces for Mini Research Write Up Assignment - -- Christina -- Spreadsheet should be in VDSstaff account (sharee by Dr. B), then 'publish' live results to Wikispaces. See last year as an example of how the results spreadsheet should look. http://vdsstream.wikispaces.com/Mini+Research+Write+Ups+Spring+12
??
make glycerol stocks of E. coli competent cells (DH5alpha and BL21(DE3) - make plates with no resistance, grow up 4ml culture, see Glycerol Stocks protocol for freezing down.
-- there is also a protocol using DMSO in the Molecular Cloning books
Week 0 workers: Andrew -
vdsstaff Google Calendar, Wikispaces protein labs template pages, supplies and reagents, starting o/n expression and making LB, setting up Pigeon Holes - DONE - Thanks!
purchasing receipts into Excel spreadsheet. - In PROGRESS Kaarthik
supplies and reagents, starting o/n expression and making LB, setting up Pigeon Holes - DONE - Thanks! Daniel
expression and lab claning, unpacking supplies and storing them - - DONE - Thanks! Michael
expression and lab claning, unpacking supplies and storing them - - DONE - Thanks! Ruifei
spin down protein expression samples - DONE - Thanks!
update laptops - DONE - Thanks!
CATALOGING PURCHASING INTO EXCEL SPREADSHEET FROM FALL 12 - ANDREW
get receipts from Dr. B
get spreadsheet template from Dr. B
GOOGLE WORK (not at Google pay rates....)
create calendars for EACH mentor/TA in GDocs - Andrew DONE - THANKS
-- maybe need to create a separate Google account (VDSstaff@gmail.com with the mentor password)
-- transfer the Mentors' schedules from the Google Spreadsheet (Scheduling MentorsforGDocsSpring13) to the calendars
-- move Dr. B's mentors calendar to this.
So, this will have all the mentors' class schedules & the mentor's work schedules in one place (make it easier to assign people times)
Make the 'Calendar for Staff' link on Wikispaces link to this calendar - but only show the Mentors (work schedule) not each mentor's individual schedule.
Update your Google calendar in VDSstaff account if you schedule has changes. Log In to VDSstaff to see it (same passwerd as regular account) - ALL MENTORS & TA
Fill in Weekly Labs to Google Calendar - Max and Aldo DONE - THANKS
(VDSclass - Class&LabTimes)
(Dr. B needs to share the calendar with you)
Fill in Assignment Due Dates to Google Calendar (VDSclass - Class&LabTimes)
Teaching Assistant's Stuff
Go over Lab Notebook Grading Rubric & Lab Notebook spreadsheet
Update student roster in GDocs Scheduling sheet - Thao (Dr. B needs to add Thao in CLIPS to all 4 classes)
Make Sign-In Sheet for Lab (for PAI 2.14 folder) - will probably be 2 sheets each week - LarryDONE - THANKS - will revise later
WIKISPACES WORK
create Wikispaces pages for each student for Protein Labs - ANDREWDONE - THANKS
Make Name Badge labels for 'Pigeon Holes' for lab notebooks - Daniel, Michael - DONE THANKS - will need to tape them after Tuesday
-- have UTEID, First Name, Last Initial
-- alphabetical order by UTEID
-- should be moveable labels so that as we add/drop people - they will still be in order
-- use Class Schedule in GDocs/Schedules to get UTEIDs and Firs Name, Last Initial
Blackbeard Blackboard Work
create TEAMS by color 7 students per Team by UTEID alphabetical? - ANDREW - DONE THanks
Misc Work
Get Gel Pump set up working
clean out top loading -20degC freezer - remove old Biobricks stuff and create a new label for VDS on a metal rack.
make -80degC freezer signs (laminate them with new laminator!)
SOLUTIONS TO MAKE:
Make LB - 2Liters - and autoclave Make 5 M NaCl - 500 ml in water, sterile filter into a bottle, label, store at Room Temp
Make Kanamycin- stocks 50ug/ul store in -20degC, Make 30 tubes of 500 ul each. Sterile filter with syringe filterbefore aliquoting into tubes. Label. Store in -20degC
Make IPTG - 1 M IPTG stock to make. Make 30 tubes of this with 500 ul in each. Label. Store in -20degC
Make Lysozyme - 20 aliquots of 500 ul at 50 mg/ml in 1.7 ml tubes. Label. Store in -20degC
Make TCEP - make ~50 x 100ul aliquots of 500 mM aliquots medium size centrifuge tubes. Label, put in a box and Store at Room Temp in cubby.
Make PMSF - 30 x 500 ul aliquots of 10mM in Isopropanol 1.7 ml tubes. Label. store in -20degC
Make Imidazole - 1M stock make in beaker of 500 ml of water, then bottle top sterile filter it into a bottle, store at Room Temp
Lysis Buffer for Sonication (make 500 ml)
(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
label, store at 4degC
NEW Wash and Elution Buffers and Storage Buffer(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Wash Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
Elution Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 300 mM
pH 8.0 w/ NaOH
FPLC column buffer - tris Also 'storage' buffer
Tris 50 mM
NaCl 150 mM
pH 8.0 w/ NaOH
Then filter sterilize
Then degass**
6X SDS Page Buffer from 5 Prime Protocol
30 ml of glycerol – add first so that you can see the volume (viscous)
(In a separate tube) - 30 ml of Nanopure water
--- 1.635 g Tris powder
--- 3 g SDS poweder
--- 0.3 g Bromophenol blue
----2.3136 g DTT
Mix contents of second tube into tube with glycerol
Add some more Nanopure water to 50 ml total final volume
Make Compounds in DMSO - 50 uM in 100% DMSO, then 5 or 10 uM
Update Laptops and Desktops
Clean off old icons from Desktops of Desktop computers
Do Windows Updates - RUIFEI -Done Thanks!
Start up laptops and do updates on them. Remove security credentials.
COMPUTER SETUP INFO:
Computer names:
Valine
Aspartate
Serine
Tryptophan
Histidine
Methionine Computer Description: FRI Laptop Username: VDSclass
Passerd: you know it already
Set up UT Restricted Wireless - sign into GUEST first then open a webpage to get forced to the Restricted installer
*Download 'RemoveCredentials.exe' to Desktop
Software that should be installed on all the computers:
Firefox [[#|Internet Explorer]] - Boo!
Chrome
- Bookmarks to install on browsers:
Gmail, UTexas, CNS, FRI, VDS Google Site, VDS Wikispaces, RT-qPCR Course, Residential Halls Study Group, PDB, BRENDA, MolPROBITY
Use FRI logo as the Desktop.
SUMMER Opportunity: The 2013 MIDAS Summer Undergraduate Research Program will be held May 20 – July 26, 2013, at the University of Pittsburgh in Pittsburgh, PA. See www.midas.pitt.edu/srp The University of Pittsburgh Models of Infectious Disease Agent Study (MIDAS) National Center of Excellence is pleased to announce a summer research opportunity for undergraduate students in the field of computational modeling and simulation of infectious diseases. Through this ten-week Summer Research Program, participants will gain an appreciation of major research questions being raised at the intersection of public health, biological science, and computer technology and become acclimated to the rigors of scientific research and graduate education. Women and underrepresented groups are particularly encouraged to apply. [[#|Application]] Deadline: March 1, 2013 For more information about the University of Pittsburgh MIDAS National Center of Excellence, go to www.midas.pitt.edu.
Sunday Jan 13th (2-6pm?)
Team Building Activity
Staff picture
VDS work - various tasks and goig through 1st labs
Dinner afterwards
Dr B - Sunday:
print my Notes
print mentor contracts
print picture roster
print 1st Teaching points - Buffers & Solutions
pritn syllabus (or just the Weekly Lab Schedule)
get sample [[#|timesheets]]
print Lab Notebook grading rubric
print 1st week Mentor Schedule
MONDAY
Pick up package in Welch supply room - Janice & Suman @ 3pm - make Kaarthik take you-Done Thanks!
Make 25 LB + AMP plates - Janice-Done Thanks!
Verify ICE room access - ISO entered on Google sheet - DANIEL-Done Thanks!
Make a Google Form - Janice-Done Thanks!
-- for voluntary sign up to do 1st Part of Lab 1 (Buffers & Solutions) at the end of this week.
TUESDAY 1st priority is Help Session for Lit Search Assignment.
Tape students' name labels into lab notebook 'Pigeon Holes' - Christina, Brandon -Done Thanks!
WEDNESDAY
Larry, Andrew, Max
Sadhana, Suman, Ruifei, Michael
1st priority is Help Session for Lit Search Assignment.
Page Ruler prestained protein MW ladder ( FERMENTAS)
Suman
4
Biosci storeroom
squirt bottles for Bee'rs Law
Ruifei
1
Biosci storeroom
Green laser pointer (not cheap)
Ruifei
spray bottles - 2
Sharpie pens (black, fine tip)??
labeling tape (thick and thin) - various colors - maybe about 10 rolls??
bleach??
alconox??
THURSDAY Sadhana, Daniel, Divya, Brandon, Michael
1st priority is Help Session for Lit Search Assignment.
Buy stuff at Biosci storeroom - Divya, Brandon
Create a Lab Safety Quiz on BlackBoard (use lab safety videos on our Wikispaces page & the questions from Dr. Procko - in GDocs/Mentors + add your own) - Sadhana
-need access to BB
Transformation of pGBR22 in DH5alpha AMP plates - - Divya
1st part of Buffers & Solutions lab and make graph for it. - Divya
Rinse the 'clean' collirollers in nanopure water, transfer to a clean bottle, label - then Autoclave (use autoclave tape) - Brandon
Autoclave Nanopure water, label, store in Cubby. Make 2 x 500ml. - this is for 1st Lab to make 30% EtOH - Brandon
Autoclave colirollers - Brandon
divide up colirrolers in to 6 rollers each in sterile tubes of (600 ul tubes) - make a full ~ 80 tube rack of these
1st priority is Lab Safety walk throughs, Help sessions for Lit Search, and Part 1 of Lab 1
1pm - visit WELCH computer guy to do OpenBabel install check - Kaarthik
Transformation of pGBR22 in BL21(DE3) Kan/Suc plates - Janice
Remove Plates of pGBR22 inDh5alphas from incubator, parafilm them and put in fridge (from Divya) - Divya
Tuesday
Pick up SDS and KH2PO4 at Biosci - Andrew
THURSDAY
grow up pGBR22 DH5alpha colony in 2x80ml of LB overnight in AMP - for Midiprep - (start this late at the end of your shift) - DANIEL - DONE Thanks
Lab Notebook grading assignments for Mentors
Make Google Docs spreadsheet in the VDSstaff Gmail account that has each UTEID and FIrst Name in a long column - DONE
Then Have a column that is the Week, then the names of the Mentors assigned to 5-6 each of the students - DONE
FRIDAY
Transform pGBR22 in BL21(DE3) in AMP plates (not kan suc!) - Sadhana
Sort Lit Search & Biblio assignments by group.- Suman
Spin down cultures of pGBR22 in DH5alpha from overnight growth and store in -20degC - (maybe Midiprep.......) SUman
Check lab safety completion for all students
-- see the printed sheets in the lab binder and then cross check them to the Wikispaces 'Required Lab Safety' page table. - RUIFEI, Janice - Sadhana (finish off)
Remove Sadhana's plates of pGBRSS in BL21(DE3), parafilm and store in 4degC - Urvashi
Check Ice Room access list - Christina
- cross reference to UTEIDs of Class Roster (can be found in VDSstaff@gmail.com account
- send email reminder with link to those that have not completed form - can use the Blackboard 'Gradebook' to check those that have not done it and send a group email to them
Midiprep (pBGR22) - Urvashi Completed -- Suman placed the pellets in the -20degC (in the door)
Mentors grade Lit Search Assignment for their TEAM
Blackboard
edit Groups and remove all but the Discussion Board, Email and File Exchange in the Tools Availability - All Team Leader mentors
Plasmids that we need to transform into DH5alpha (from Mini-prep DNA)
YopH in pNIC-Bsa4 - we have Mini-prep DNA in Final Plasmids box
DH5alpha colonies that we need to grow up 2x 80 ml of LB o/n with Appropriate Antibiotic - for Midiprep
YopH in pNIC-Bsa4 - Kanamycin
FtHap in pNIC-Bsa4 - Kanamycin
Colirollers - autoclave and distribute to small 600 ul tubes (~6 per tube)
For Lysis Buffer (with BPer - not 'sonication' buffer) 50 mg/ml Lysozyme in 500 ul aliquots in 1.7 ml tubes. Store in -20degC
TCEP aliquots (already at 500 mM - just move from glass vials to tubes and store at Room Temp in cubby)
PMSF in 500 ul aliquots in 1.7 ml tubes (10mM concentration in isopropanol) store in -20degC
1M Imidazole (make in water) store at Room Temp
5 M NaCl (make in water) store at Room Temp
NEW Wash and Elution Buffers and Storage Buffer(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Wash Buffer Tris 100 mM NaCl 300 mM Imidazole 30 mM pH 8.0 w/ NaOH
Elution Buffer Tris 100 mM NaCl 300 mM Imidazole 300 mM pH 8.0 w/ NaOH
FPLC column buffer - tris Also 'storage' buffer**
Tris 50 mM
NaCl 150 mM
pH 8.0 w/ NaOH
Then filter sterilize
Then degass
Mentor Info and Tasks:
VDS Mentors rule!
ANDREW, ALDO, BRANDON, DANIEL, DIVYA, JANICE, MAX, MICHAEL, SUMAN, URVASHICalendar For Staff Link
Teaching Points for Labs Spring 13
-- contains lab handout and teaching points sheetNOTE: the best way to figure out what you need to work on is to do 'Ctrl+F' and search for your name. Hit 'enter' to find the next instance. - Thanks, Dr. B
----- this assumes I haven't misspelled your name!
'Starter Questions' for the TEAM meetings - to help your students get to know you better
QUESTIONS FOR THE WHOLE GROUP
General points to cover (by the TEAM leaders):
- basic intro (major, year, etc.)- overview of what they can expect from VDS (short- and long-term)
- how VDS has helped you and why it is beneficial for them to stick with it
- your research interests and experiences
- your career plans and what stage you are at now
- Why VDS is the best stream!
Printer Installation
- Login as Mentor, Start Menu,
- Devices And printers
- Add New Printer
- Add "local" printer
- Create New Port --> standard TCP pathway
- Enter IP 128.82.195.186
- Printer Name Lexmark C543
- Add Printer (if can't find printer do Window Update)
For installation of a different Printer (such as Dell) change the IP address and Printer NamePrinter Name: Lexmark C543 IP: 128.83.195.186
Printer Name: Dell IP: 129.116.152.49
Saturday 2.16
-NaOH and Tris
(from the first lab)
1L each
SATURDAY (2/2)
Make the different Stock and Dilutions for Beer's Law Unknown Experiment - Urvashi
Thao and Urvashi - I placed extra Ink, toner and paper for the Printer in the lab so that the students can print their PyMol assignment - Thanks, Dr. B
@5pm - close lab and check if any are missing labnotebooks (if they are - put a note on the LabNotebookGrading_VDS_Sp13 spreadsheet on GDocs for VDSstaff@gmail.com (use mentor password)
.
ANYTIME
Test VS3 protocol - Christina (a non CS person will do it next)Make Mini-Research Write Up Wikipages for each student (use their Disease name as the name of the page)
Create Voting forms for MiniResearch Wiki Assign
Update the Google Site for VDS - Larry
- put new Forum posters there.
Check your growth of pGBR22 in BL21(DE3) from overnight as a test for 'purple' color - (check today and tomorrow - how long does it take to go purple?) -
Grow up pGBR22 in BL21(DE3) overnight in Kan as a test for 'purple' color (start this late at the end of your shift)
Wikispaces
- Make a 'bracket' by Teams for doing MiniResearch WriteUp Wiki assign competition -Christina
- Mini Research Wiki post templates - can do this after we have chosen all of the Diseases - Christina
- '20 questions' form - can do this after we have chosen all of the Diseases
Embed Google Spreadsheet into Wikispaces for Mini Research Write Up Assignment - -- Christina-- Spreadsheet should be in VDSstaff account (sharee by Dr. B), then 'publish' live results to Wikispaces. See last year as an example of how the results spreadsheet should look.
http://vdsstream.wikispaces.com/Mini+Research+Write+Ups+Spring+12
The form is already linked to this page
http://vdsstream.wikispaces.com/Mini+Research+Write+Ups+Spring+13
??
make glycerol stocks of E. coli competent cells (DH5alpha and BL21(DE3) - make plates with no resistance, grow up 4ml culture, see Glycerol Stocks protocol for freezing down.
-- there is also a protocol using DMSO in the Molecular Cloning books
Week 0 workers:
Andrew -
vdsstaff Google Calendar, Wikispaces protein labs template pages, supplies and reagents, starting o/n expression and making LB, setting up Pigeon Holes - DONE - Thanks!
purchasing receipts into Excel spreadsheet. - In PROGRESS
Kaarthik
supplies and reagents, starting o/n expression and making LB, setting up Pigeon Holes - DONE - Thanks!
Daniel
expression and lab claning, unpacking supplies and storing them - - DONE - Thanks!
Michael
expression and lab claning, unpacking supplies and storing them - - DONE - Thanks!
Ruifei
spin down protein expression samples - DONE - Thanks!
update laptops - DONE - Thanks!
CATALOGING PURCHASING INTO EXCEL SPREADSHEET FROM FALL 12 - ANDREW
get receipts from Dr. B
get spreadsheet template from Dr. B
GOOGLE WORK (not at Google pay rates....)
create calendars for EACH mentor/TA in GDocs - Andrew DONE - THANKS-- maybe need to create a separate Google account (VDSstaff@gmail.com with the mentor password)
-- transfer the Mentors' schedules from the Google Spreadsheet (Scheduling MentorsforGDocsSpring13) to the calendars
-- move Dr. B's mentors calendar to this.
So, this will have all the mentors' class schedules & the mentor's work schedules in one place (make it easier to assign people times)
Make the 'Calendar for Staff' link on Wikispaces link to this calendar - but only show the Mentors (work schedule) not each mentor's individual schedule.
Update your Google calendar in VDSstaff account if you schedule has changes. Log In to VDSstaff to see it (same passwerd as regular account) - ALL MENTORS & TA
Fill in Weekly Labs to Google Calendar - Max and Aldo
DONE - THANKS
(VDSclass - Class&LabTimes)
(Dr. B needs to share the calendar with you)
Fill in Assignment Due Dates to Google Calendar (VDSclass - Class&LabTimes)
Teaching Assistant's Stuff
Go over Lab Notebook Grading Rubric & Lab Notebook spreadsheetUpdate student roster in GDocs Scheduling sheet - Thao (Dr. B needs to add Thao in CLIPS to all 4 classes)
Make Sign-In Sheet for Lab (for PAI 2.14 folder) - will probably be 2 sheets each week - Larry DONE - THANKS - will revise later
WIKISPACES WORK
Make Name Badge labels for 'Pigeon Holes' for lab notebooks - Daniel, Michael - DONE THANKS - will need to tape them after Tuesday
-- have UTEID, First Name, Last Initial-- alphabetical order by UTEID
-- should be moveable labels so that as we add/drop people - they will still be in order
-- use Class Schedule in GDocs/Schedules to get UTEIDs and Firs Name, Last Initial
Blackbeard Blackboard Work
create TEAMS by color 7 students per Team by UTEID alphabetical? - ANDREW - DONE THanks
Misc Work
Get Gel Pump set up workingclean out top loading -20degC freezer - remove old Biobricks stuff and create a new label for VDS on a metal rack.
For Spring 2013 Semester: - done Thanks! - Dr. B
Please Enter your class schedules on the Google Docs Spreadsheet Mentor Scheduling Sp13Each mentor (paid)
Generate [[#|time sheets]]Prepare MENTORS folder in lab:
make [[#|name badges]] and print - Daniel & Brandon - Done - just need better/new badge holders
Timesheet Pay Periods and Due Dates (see bottom of link) - Sadhana
Please Print, Read and Sign the Mentor Contracts. Then return to Dr. B
Mentor Contract on GDocs
ToDo List
Troubleshoot Labs
-Wet Labs- Buffers & Solutions -
- First pipetting steps with Excel graph of Buffers & Solutions - Janice (Mon), Divya (Thursday)
- 200 ml 0.1 M Tris Base pH 7.5 – pH meter, acids (calibrate pH meter as part of this, test out new pH probes)
- Kanamycin – syringe filter
- Beer's Law
- Buffer Titration
-Virtual LabsPyMol (1 & 2 & 3)
VS1 - Ruifei - DONE Thanks
VS2
VS3
make -80degC freezer signs (laminate them with new laminator!)
SOLUTIONS TO MAKE:
Make LB - 2Liters - and autoclave
Make 5 M NaCl - 500 ml in water, sterile filter into a bottle, label, store at Room Temp
Make Kanamycin- stocks 50ug/ul store in -20degC, Make 30 tubes of 500 ul each. Sterile filter with syringe filterbefore aliquoting into tubes. Label. Store in -20degC
Make IPTG - 1 M IPTG stock to make. Make 30 tubes of this with 500 ul in each. Label. Store in -20degC
Make Lysozyme - 20 aliquots of 500 ul at 50 mg/ml in 1.7 ml tubes. Label. Store in -20degC
Make TCEP - make ~50 x 100ul aliquots of 500 mM aliquots medium size centrifuge tubes. Label, put in a box and Store at Room Temp in cubby.
Make PMSF - 30 x 500 ul aliquots of 10mM in Isopropanol 1.7 ml tubes. Label. store in -20degC
Make Imidazole - 1M stock make in beaker of 500 ml of water, then bottle top sterile filter it into a bottle, store at Room Temp
Lysis Buffer for Sonication (make 500 ml)
(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
label, store at 4degC
NEW Wash and Elution Buffers and Storage Buffer(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Wash Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
Elution Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 300 mM
pH 8.0 w/ NaOH
FPLC column buffer - tris Also 'storage' buffer
Tris 50 mM
NaCl 150 mM
pH 8.0 w/ NaOH
Then filter sterilize
Then degass**
6X SDS Page Buffer from 5 Prime Protocol
30 ml of glycerol – add first so that you can see the volume (viscous)(In a separate tube) - 30 ml of Nanopure water
--- 1.635 g Tris powder
--- 3 g SDS poweder
--- 0.3 g Bromophenol blue
----2.3136 g DTT
Mix contents of second tube into tube with glycerol
Add some more Nanopure water to 50 ml total final volume
Make Compounds in DMSO - 50 uM in 100% DMSO, then 5 or 10 uM
Update Laptops and Desktops
Clean off old icons from Desktops of Desktop computersDo Windows Updates - RUIFEI - Done Thanks!
Start up laptops and do updates on them. Remove security credentials.
COMPUTER SETUP INFO:
Computer names:Valine
Aspartate
Serine
Tryptophan
Histidine
Methionine
Computer Description: FRI Laptop
Username: VDSclass
Passerd: you know it already
- Set up UT Restricted Wireless - sign into GUEST first then open a webpage to get forced to the Restricted installer
*Download 'RemoveCredentials.exe' to DesktopSoftware that should be installed on all the computers:
- Microsoft Forefront Client Security - Bevoware
Secure Shell - BevowarePutty
Xming - with MESA and Xming Fonts:
http://www.straightrunning.com/XmingNotes/
- Microsoft Office 2007 - Dr. B has CD
PyMol - on our Google DocsWinSCP
7-zip
Logger Pro ve. 8.3 - Dr. B has USB thumb drive with this
- Viia7 v 1.2 software for RT-qPCR - install software - then get key from Dr. B
http://www.appliedbiosystems.com/absite/us/en/home/support/software/real-time-pcr/viia7-software.htmlFirefox
[[#|Internet Explorer]] - Boo!
Chrome
- Bookmarks to install on browsers:
Gmail, UTexas, CNS, FRI, VDS Google Site, VDS Wikispaces, RT-qPCR Course, Residential Halls Study Group, PDB, BRENDA, MolPROBITY
Use FRI logo as the Desktop.
SUMMER Opportunity:
The 2013 MIDAS Summer Undergraduate Research Program will be held May 20 – July 26, 2013, at the University of Pittsburgh in Pittsburgh, PA.
See www.midas.pitt.edu/srp
The University of Pittsburgh Models of Infectious Disease Agent Study (MIDAS) National Center of Excellence is pleased to announce a summer research opportunity for undergraduate students in the field of computational modeling and simulation of infectious diseases. Through this ten-week Summer Research Program, participants will gain an appreciation of major research questions being raised at the intersection of public health, biological science, and computer technology and become acclimated to the rigors of scientific research and graduate education. Women and underrepresented groups are particularly encouraged to apply.
[[#|Application]] Deadline: March 1, 2013
For more information about the University of Pittsburgh MIDAS National Center of Excellence, go to www.midas.pitt.edu.
Sunday Jan 13th (2-6pm?)
Team Building ActivityStaff picture
VDS work - various tasks and goig through 1st labs
Dinner afterwards
Dr B - Sunday:
print my Notes
print mentor contracts
print picture roster
print 1st Teaching points - Buffers & Solutions
pritn syllabus (or just the Weekly Lab Schedule)
get sample [[#|timesheets]]
print Lab Notebook grading rubric
print 1st week Mentor Schedule
MONDAY
Pick up package in Welch supply room - Janice & Suman @ 3pm - make Kaarthik take you - Done Thanks!
Make 25 LB + AMP plates - Janice- Done Thanks!
Verify ICE room access - ISO entered on Google sheet - DANIEL- Done Thanks!
Make a Google Form - Janice- Done Thanks!
-- for voluntary sign up to do 1st Part of Lab 1 (Buffers & Solutions) at the end of this week.
TUESDAY
1st priority is Help Session for Lit Search Assignment.
Tape students' name labels into lab notebook 'Pigeon Holes' - Christina, Brandon - Done Thanks!
WEDNESDAY
Larry, Andrew, Max
Sadhana, Suman, Ruifei, Michael
1st priority is Help Session for Lit Search Assignment.
Wikispaces - edit Lab Safety Page - Max- DONE - Thanks!
Change VDSstaff password GDOcs account to: the mentor passwerd - Andrew- FAIL- Thanks!
Change passwerds on laptops to new VDSclass passwerd - Andrew- DONE - Thanks!
Enough plates for expression lab - Michael, Ruifei- DONE - Thanks!
PURCHASING at BioScience Storeroom (NHB) - for Thurs
spray bottles - 2
Sharpie pens (black, fine tip)??
labeling tape (thick and thin) - various colors - maybe about 10 rolls??
bleach??
alconox??
PURCHASING at BioScience Storeroom (NHB) - for Thurs
spray bottles - 2
Sharpie pens (black, fine tip)??
labeling tape (thick and thin) - various colors - maybe about 10 rolls??
bleach??
alconox??
THURSDAY
Sadhana, Daniel, Divya, Brandon, Michael
1st priority is Help Session for Lit Search Assignment.
Buy stuff at Biosci storeroom - Divya, Brandon
Create a Lab Safety Quiz on BlackBoard (use lab safety videos on our Wikispaces page & the questions from Dr. Procko - in GDocs/Mentors + add your own) - Sadhana
-need access to BB
Transformation of pGBR22 in DH5alpha AMP plates - - Divya
1st part of Buffers & Solutions lab and make graph for it. - Divya
Rinse the 'clean' collirollers in nanopure water, transfer to a clean bottle, label - then Autoclave (use autoclave tape) - Brandon
Autoclave Nanopure water, label, store in Cubby. Make 2 x 500ml. - this is for 1st Lab to make 30% EtOH - Brandon
Autoclave colirollers - Brandon
- divide up colirrolers in to 6 rollers each in sterile tubes of (600 ul tubes) - make a full ~ 80 tube rack of these
FRIDAYJoey, Ruifei, Divya Kaarthik
Larry, Andrew, Urvashi
1st priority is Lab Safety walk throughs, Help sessions for Lit Search, and Part 1 of Lab 1
1pm - visit WELCH computer guy to do OpenBabel install check - Kaarthik
Transformation of pGBR22 in BL21(DE3) Kan/Suc plates - Janice
Remove Plates of pGBR22 inDh5alphas from incubator, parafilm them and put in fridge (from Divya) - Divya
Tuesday
Pick up SDS and KH2PO4 at Biosci - AndrewTHURSDAY
grow up pGBR22 DH5alpha colony in 2x80ml of LB overnight in AMP - for Midiprep - (start this late at the end of your shift) - DANIEL - DONE ThanksLab Notebook grading assignments for Mentors
Make Google Docs spreadsheet in the VDSstaff Gmail account that has each UTEID and FIrst Name in a long column - DONEThen Have a column that is the Week, then the names of the Mentors assigned to 5-6 each of the students - DONE
FRIDAY
Transform pGBR22 in BL21(DE3) in AMP plates (not kan suc!) - SadhanaSort Lit Search & Biblio assignments by group.- Suman
Spin down cultures of pGBR22 in DH5alpha from overnight growth and store in -20degC - (maybe Midiprep.......) SUman
Check lab safety completion for all students
-- see the printed sheets in the lab binder and then cross check them to the Wikispaces 'Required Lab Safety' page table. - RUIFEI, Janice - Sadhana (finish off)Remove Sadhana's plates of pGBRSS in BL21(DE3), parafilm and store in 4degC - Urvashi
Check Ice Room access list - Christina
- cross reference to UTEIDs of Class Roster (can be found in VDSstaff@gmail.com account
- send email reminder with link to those that have not completed form - can use the Blackboard 'Gradebook' to check those that have not done it and send a group email to them
Midiprep (pBGR22) - Urvashi Completed
-- Suman placed the pellets in the -20degC (in the door)
Mentors grade Lit Search Assignment for their TEAM
Blackboard
edit Groups and remove all but the Discussion Board, Email and File Exchange in the Tools Availability - All Team Leader mentorsOLD STUFF (ALL OF 2012)
Mentors2012OLD STUFF (Fall 2011):
Plasmids that we have as Midi Prep
Plasmids that we need to transform into DH5alpha (from Mini-prep DNA)
YopH in pNIC-Bsa4 - we have Mini-prep DNA in Final Plasmids box
DH5alpha colonies that we need to grow up 2x 80 ml of LB o/n with Appropriate Antibiotic - for Midiprep
YopH in pNIC-Bsa4 - Kanamycin
FtHap in pNIC-Bsa4 - Kanamycin
Colirollers - autoclave and distribute to small 600 ul tubes (~6 per tube)
REAGENTS THAT WE NEED:
Make ProtocolHomemadeSDSPageGelSolutionsVDS_Fall11.docx gels
Tris-acetate buffer that is 500 mM pH 5.5 - see Solutions&DilutionsforGdocs spreadsheet
LB media - autoclaved
LB/Kan/Suc plates
For Lysis Buffer (with BPer - not 'sonication' buffer)
50 mg/ml Lysozyme in 500 ul aliquots in 1.7 ml tubes. Store in -20degC
TCEP aliquots (already at 500 mM - just move from glass vials to tubes and store at Room Temp in cubby)
PMSF in 500 ul aliquots in 1.7 ml tubes (10mM concentration in isopropanol) store in -20degC
1M Imidazole (make in water) store at Room Temp
5 M NaCl (make in water) store at Room Temp
NEW Wash and Elution Buffers and Storage Buffer(see GDocs 'Solutions&Dilutions' in /Misc folder for calculations)
Wash Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 30 mM
pH 8.0 w/ NaOH
Elution Buffer
Tris 100 mM
NaCl 300 mM
Imidazole 300 mM
pH 8.0 w/ NaOH
FPLC column buffer - tris Also 'storage' buffer**
Tris 50 mM
NaCl 150 mM
pH 8.0 w/ NaOH
Then filter sterilize
Then degass